[2026-06-08T07:24:25] Launching Arriba 2.4.0
[2026-06-08T07:24:25] Loading assembly from 'ref_genome.fa' 
[2026-06-08T07:24:46] Loading annotation from 'ref_annot.gtf' 
[2026-06-08T07:24:52] Reading chimeric alignments from 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam' (total=1584479)
[2026-06-08T07:25:26] Marking multi-mapping alignments (marked=1367866)
[2026-06-08T07:25:27] Detecting strandedness (no)
[2026-06-08T07:25:27] Annotating alignments 
[2026-06-08T07:25:36] Filtering duplicates (remaining=423356)
[2026-06-08T07:25:37] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=330886)
[2026-06-08T07:25:37] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=330886)
[2026-06-08T07:25:37] Filtering viral contigs with expression lower than the top 5 (remaining=330886)
[2026-06-08T07:25:38] Filtering viral contigs with less than 5% coverage (remaining=330886)
[2026-06-08T07:25:39] Estimating fragment length (mate gap mean=-41.8918, mate gap stddev=24.5478, read length mean=80.5062)
[2026-06-08T07:25:39] Filtering read-through fragments with a distance <=10000bp (remaining=325345)
[2026-06-08T07:25:40] Filtering inconsistently clipped mates (remaining=306889)
[2026-06-08T07:25:40] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=283341)
[2026-06-08T07:25:41] Filtering fragments with small insert size (remaining=282595)
[2026-06-08T07:25:41] Filtering alignments with long gaps (remaining=282595)
[2026-06-08T07:25:41] Filtering fragments with both mates in the same gene (remaining=282076)
[2026-06-08T07:25:42] Filtering fusions arising from hairpin structures (remaining=259882)
[2026-06-08T07:25:42] Filtering reads with a mismatch p-value <=0.01 (remaining=41904)
[2026-06-08T07:25:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=13236)
[2026-06-08T07:25:44] Finding fusions and counting supporting reads (total=13614)
[2026-06-08T07:25:46] Merging adjacent fusion breakpoints (remaining=13454)
[2026-06-08T07:25:47] Filtering multi-mapping fusions by alignment score and read support (remaining=5124)
[2026-06-08T07:25:52] Estimating expected number of fusions by random chance (e-value) 
[2026-06-08T07:25:53] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=4966)
[2026-06-08T07:25:53] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=4087)
[2026-06-08T07:25:53] Filtering fusions with <2 supporting reads (remaining=128)
[2026-06-08T07:25:53] Filtering fusions with an e-value >=0.3 (remaining=51)
[2026-06-08T07:25:53] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=51)
[2026-06-08T07:25:54] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=33)
[2026-06-08T07:25:54] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=33)
[2026-06-08T07:25:54] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=27)
[2026-06-08T07:25:55] Searching for fusions with spliced split reads (remaining=27)
[2026-06-08T07:25:56] Selecting best breakpoints from genes with multiple breakpoints (remaining=24)
[2026-06-08T07:25:56] Filtering read-through fusions with breakpoints near the gene boundary (remaining=24)
[2026-06-08T07:25:56] Searching for fusions with >=4 spliced events (remaining=24)
[2026-06-08T07:25:56] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8)
[2026-06-08T07:26:17] Filtering fusions with anchors <=23nt (remaining=5)
[2026-06-08T07:26:17] Filtering end-to-end fusions with low support (remaining=5)
[2026-06-08T07:26:17] Filtering fusions with no coverage around the breakpoints (remaining=5)
[2026-06-08T07:26:17] Indexing gene sequences 
[2026-06-08T07:26:17] Filtering genes with >=30% identity (remaining=4)
[2026-06-08T07:26:17] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=0)
[2026-06-08T07:26:18] Selecting best breakpoints from genes with multiple breakpoints (remaining=0)
[2026-06-08T07:26:18] Searching for additional isoforms (remaining=0)
[2026-06-08T07:26:18] Assigning confidence scores to events 
[2026-06-08T07:26:18] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-06-08T07:26:18] Writing fusions to file 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.tsv' 
[2026-06-08T07:26:19] Writing discarded fusions to file 'ColoN_FFPE_L03_RNA_01_B23LG7FLT4_1.arriba.fusions.discarded.tsv'
[2026-06-08T07:26:22] Freeing resources
[2026-06-08T07:26:26] Done (elapsed time=00:02:01, CPU time=00:01:59, peak memory=5.63gb)